Japan's capital is a compelling study in contrasts—sprawling yet full of intimate neighborhoods; ancient yet up-to-the-minute. Here's how to navigate its riches.

"I have been in Japan for two weeks," Albert Einstein wrote in 1922 while on a train departing Tokyo, "and yet there are as many mysterious things as on the first day." Nearly a century later, this megalopolis still strikes many visitors as mysterious and impenetrable. Teeming with nearly 13 million people and covering 844 square miles, the city is knotted with close to 50 train lines and legions of neighborhoods, each its own universe with its own style and subculture.

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"Visitors can get overwhelmed by the general sensory overload," acknowledges Charles Spreckley, the British-born cofounder of Bespoke Tokyo, a custom concierge service, and the former editor in chief of Metropolis, Japan's biggest English-language magazine. "So many people, new noises, different smells and sounds, and so many exotic Asian signs, interspersed with random English words. It's all vaguely familiar but also extremely foreign, which is a beguiling mix."

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When most people picture Tokyo—the city portrayed in movies and pop culture—they're probably thinking of Shinjuku and Shibuya, the manic, densely populated areas that reputedly inspired Ridley Scott's film Blade Runner, and where Sofia Coppola shot much of 2003's Lost in Translation. But if you look past the slick, futuristic façade and venture into other neighborhoods, you'll discover a ­different Tokyo. It's a layered, complex place that quietly maintains elaborate ancient customs and etiquette—bowing, gift-giving, chopstick usage—and reveals itself gradually. Amid the neon-streaked skyscrapers and throbbing commercial districts are tranquil shrines, temples, gardens, and parks (the 130-acre Ueno Park, for one, is home to several museums and, in spring, ablaze with cherry blossoms). These yield unexpected moments of peace, along with the many lanes of small wooden houses that give the city "a sense of human scale," says Kengo Kuma, one of Japan's most celebrated architects.

Hard to believe, but Tokyo started out, in the 12th century, as a sleepy fishing village. Situated off the banks of Tokyo Bay and originally known as Edo, it began its transformation in 1868, when Emperor Meiji transferred the seat of imperial power there from Kyoto, triggering a push toward rapid industrialization. Steady urban development was interrupted by two major events in the early and mid-1900s: the epic Great Kanto earthquake of 1923, one of the most deadly in history; and the firebombing by American troops during World War II, which devastated more than half the city. In both cases, Tokyo pulled itself from the rubble and rebuilt, metamorphosing over the next half-century from third-world status into an international powerhouse.

It does face some challenges, including the recent economic downturn, no small blow to a country still recovering from a recession triggered by a real-estate crash in the '90s. Booming Asian markets are eclipsing Japan's, and China is poised to overtake it as the world's second-largest economy. But when it comes to sheer style and influence in the realms of fashion, food, architecture, and design, Tokyo is thriving.

This year, the Michelin Guide awarded more stars to the city's restaurants—261 total—than to any place in the world, cementing its reputation as a global gastronomic capital renowned for perfectionist chefs and high-quality ingredients. The maximum three stars went to a range of dining establishments, from the humble Sushi Mizutani, a ten-seat sushi bar tucked away in the basement of an office building, to the refined Japanese-inflected French restaurant Quintessence, helmed by wunderkind chef Shuzo Kishida. But you don't have to eat at a posh place to immerse yourself in Tokyo's rich culinary scene: Simply wander the labyrinthine aisles of a depachika, as the basement food halls of department stores are called, where everything from the pickled squid to the cream puffs is impeccably prepared and presented, and you'll understand why it's a foodie mecca.

A slew of new hotels have opened in the past few years, featuring decor that puts a fresh, modern spin on traditional materials and aesthetics. At the Peninsula Tokyo, which debuted in 2007 and is a stone's throw from the Imperial Palace, interior designer Yukio Hashimoto aimed to "create spaces where you can rediscover Japanese culture in a brand-new way," incorporating horse-chestnut sliding doors in guest rooms and upholstery from a kimono designer in the lobby. At the four-year-old Mandarin Oriental, textile artist Reiko Sudo swathed the interiors in custom-made fabrics also inspired by kimono patterns as well as nature motifs. Even the über-hip contemporary Claska hotel recently unveiled three minimalist rooms outfitted with tatami mats, futon-style platform beds, and classic Noguchi lamps.

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Though you'll still spot some women gliding down the sidewalk wearing traditional Japanese garments, the style here is generally wilder and more fad-driven. "In Tokyo fashion, transitions are very fast, and people are fickle," says Dai Fujiwara, the creative director of Issey Miyake. "Attention tends to move from one thing to the next, quickly. That's part of what makes our fashion scene so interesting." This hunger for novelty is also fed by the high cost of real estate. "Because most Tokyoites live in tiny apartments, they spend more time out and about," Spreckley explains. "That means they are always looking for new things to do, new stimulation­­­—whether through clothing, food, or hobbies. Trends become a sort of social discourse among peers." Currently in vogue are collagen-enriched drinks and foods (supposedly good for the skin), young men wearing long skirts (yes, really), and outfits inspired by bike messengers, such as cycling trousers worn under cargo shorts with one leg rolled up.

Needless to say, the city offers some of the best people-watching on the planet. "The most interesting fashion is always on the streets," says Tomoaki "Nigo" Nagao, one of Japan's most influential pop-culture entrepreneurs. He founded the cult urban-clothing company A Bathing Ape 17 years ago in the Harajuku district, ground zero for the city's trend-obsessed youth. "We have a hunger for foreign influences and a unique ability to assimilate and reinterpret them. The process is often reverential, but the end product is always uniquely Tokyo," he says. For an extreme example, witness the famous "cosplay" gangs, who gather on the Jingu bridge to preen and pose, exuberantly dressed as manga and anime (Japanese comics and animation) characters or Victorian-inspired "gothic Lolitas," complete with petticoats, parasols, and tottering platform shoes.

Harajuku and its more upscale neighbor Aoyama have become increasingly commercial over the years, but you'll still find independent shops peppering the side streets that branch off Omotesando, a broad, tree-lined avenue that's Tokyo's equivalent of the Champs-Élysées. Sticking to the main drag, you'll discover all the boldface brands, some housed in architectural marvels that draw as many design buffs as deep-pocketed shoppers. Among them are a Louis Vuitton flagship created by Jun Aoki to resemble a stacked pile of tra­veling trunks, and the bulbous, honeycombed Prada store by Herzog & de Meuron. Last fall, the area unveiled yet another architectural icon: Kengo Kuma's exquisite Nezu Museum. The small, sloping building is clad in glass, dark steel, and bamboo; its six galleries showcase Japanese and East Asian art and crafts from the private collection of the late industrialist Nezu Kaichiro. In front of the structure is a bustling street; behind is a lovely Japanese garden with teahouses and a café. In this way, Kuma says, the museum acts as a symbolic "gate connecting the city and the sacred garden."

Roppongi, home to feudal lords in the Edo period and leveled during World War II, now gleams with luxe shopping centers, expensive real estate, and expat nightlife. More recently, it has emerged as a cultural center, starting with the opening of the Mori Art Museum in 2003. Four years later came the curvaceous glass National Art Center, the crafts-focused Suntory Museum of Art, and 21_21 Design Sight, an experimental arts space run by the Issey Miyake Foundation.

West of Roppongi is a less-explored and quieter pocket of neighborhoods that includes Nakameguro, bisected by a canal whose adjacent streets are dotted with cherry trees and stores and cafés. In nearby Daikanyama, a hip enclave of boutiques, don't miss shops such as Okura, where hand-dyed indigo clothing dangles from scraps of driftwood suspended from the ceiling, and CA4LA, a hat emporium chockablock with stylish bowlers and fedoras.

To the northeast is Asakusa, home to a plethora of Buddhist and Shinto temples and shrines, including the city's oldest, the 7th-century incense-scented Senso-ji. Also definitely worth a wander is Kappabashi, a nearby street devoted entirely to restaurant-supply shops, where you can pick up traditional Japanese kitchen tools like an earthenware suribachi (mortar) and wooden surikogi (pestle), as well as the glossily realistic plastic food so prominently displayed outside sushi and noodle restaurants.

From there, head to Akihabara, where bright, flashing stores brim with electronics, manga, and anime, and armies of pigtailed young women dressed as French maids lure passersby into themed "maid cafés." The Tokyo-based artist Takashi Mur­akami, who is known for edgy sculptures and paintings and has splashed his signature cartoonish characters across Louis Vuitton purses, draws inspiration from the district's vibrant otaku (geek) culture, labeling it "a true Japanese original."

It's the abundance of compelling and often-hidden corners that induces adoration by visitors and residents alike. "I love Tokyo because I still discover new surprises each time I go, after all these years," says Masako Shinn, a trustee at the Japan Society in New York and a partner at the visual-arts book publisher Graphis. "The city is like a giant Chinese medicine cabinet with hundreds of little drawers. You never know what's going to be inside each new drawer you open."

Eat sushi at dawn. At Tsukiji, the world's largest fish market (www.tsukiji-market.or.jp), take in the ­bustling stalls and auctions, then head to tiny Sushi Dai for breakfast (5-2-1 Tsukiji, Chuo-ku, 3-3547-6797).

Think big. More than just gigantic under-clad wrestlers, sumo is a revered national sport. Attend seasonal tournaments or visit local sumo stables to watch training (www.sumo.or.jp).

Ginza Yoshimizu, 3-11-3 Ginza, Chuo-ku, 3-3248-4432; yoshimizu.com: Bamboo floors, yukata robes, and homemade Japanese meals ensure this modern version of a ryokan (traditional inn) is a tranquil retreat.